What happened to The Governor, Martinez, and Shupert?
My personal opinion is that they will stumble upon a National Guard armory and they will gather weapons, fuel, and cars
What's going to be done with the citizens of Woodbury at the Prison?
The elders will be a problem since they need constant attention, but the others will probably become an asset to Rick by being able to shoot, etc. I think we'll see Dr. Stevens there too, and she'll be an asset when it comes to people in need of medical attention.
What will the Governor do to get his revenge?
I think he'll assemble a group of 10-12 hardened survivors, with the promise of a safe haven (the Prison) and supplies (the guns, fuel, etc). In order to get them to follow the Governor, Martinez and Shupert will mount a raid on them wearing masks, and the Governor will blame it on Rick's group.
What will happen with the prison?
I believe it will be cleaned up, the fences repaired, and they'll patch up the breaches. Most likely they'll clear out the tombs and they could find more smoke grenades, tear gas, and weapons. They could fortify it better lining the fences with wood and sheet metal.
Who is Roy Stark and what role will he play? And how will he be introduced?
Roy Stark will most likely be Abraham, or something like him. He in my opinion will be a slight right hand man to Rick along with Tyreese and Daryl. After one of the two dies he will be a full right hand man to him. As for how he'll be introduced, maybe while on a supply run he is come across by the Prison. Or he could be part of the Governor's plans, but after he finds out what the Governor is really up to and what he has done he flees to the Prison.
Will Morales Return, What Will Happen With Morgan?
I think Morales will return early in Season 4, he won't go directly to the prison, they will most likely uncover him during a supply run, or he could be part of the group that the Governor tries to recruit (that would be intresting).
As for Morgan, maybe when Rick gets run out of the prison, they will go to Morgan's fortified town for temporary shelter.
How Should Season 4 Begin?
It would be cool if it would start with a flashback, maybe the beginnings of Woodbury, or with the Governor driving into a town with Martinez and Shupert desperate for food, and they stumble upon the National Guard armory, kind of like in 3x1, desperate they stumble on the Prison.